Root Gravitropism Is Regulated by a Crosstalk between para-Aminobenzoic Acid, Ethylene, and Auxin

OsNAC121 regulates root development, tillering, panicle morphology, and grain filling in rice plant

Transcription factors in coordination with phytohormones form an intricate regulatory network modulating vital cellular mechanisms like development, growth and senescence in plants. In this study, we have functionally characterized the transcription factor OsNAC121 by developing gene silencing and overexpressing transgenic rice plants, followed by detailed analyses of the plant architecture. Transgenic lines exhibited remodelling in crown root development, lateral root structure and density, tiller height and number, panicle and grain morphologies, underpinning the imbalanced auxin: cytokinin ratio due to perturbed auxin transportation. Application of cytokinin, auxin and abscisic acid increased OsNAC121 gene expression nearly 17-, 6- and 91-folds, respectively. qRT-PCR results showed differential expressions of auxin and cytokinin pathway genes, implying their altered levels. A 47-fold higher expression level of OsNAC121 during milky stage in untransformed rice, compared to 14-day old shoot tissue, suggests its crucial role in grain filling; as evidenced by a large number of undeveloped grains produced by the gene silenced lines. Crippled gravitropic response by the transgenic plants indicates their impaired auxin transport. Bioinformatics revealed that OsNAC121 interacts with co-repressor (TOPLESS) proteins and forms a part of the inhibitor complex OsIAA10, an essential core component of auxin signalling pathway. Therefore, OsNAC121 emerges as an important regulator of various aspects of plant architecture through modulation of crosstalk between auxin and cytokinin, altering their concentration gradient in the meristematic zones, and consequently modifying different plant organogenesis processes.

Trichoderma-secreted anthranilic acid promotes lateral root development via auxin signaling and RBOHF-induced endodermal cell wall remodeling

Trichoderma spp. have evolved the capacity to communicate with plants by producing various secondary metabolites (SMs). Nonhormonal SMs play important roles in plant root development, while specific SMs from rhizosphere microbes and their underlying mechanisms to control plant root branching are still largely unknown. In this study, a compound, anthranilic acid (2-AA), is identified from T. guizhouense NJAU4742 to promote lateral root development. Further studies demonstrate that 2-AA positively regulates auxin signaling and transport in the canonical auxin pathway. 2-AA also partly rescues the lateral root numbers of CASP1pro:shy2-2, which regulates endodermal cell wall remodeling via an RBOHF-induced reactive oxygen species burst. In addition, our work reports another role for microbial 2-AA in the regulation of lateral root development, which is different from its better-known role in plant indole-3-acetic acid biosynthesis. In summary, this study identifies 2-AA from T. guizhouense NJAU4742, which plays versatile roles in regulating plant root development.

Arabidopsis Root Development Regulation by the Endogenous Folate Precursor, Para-Aminobenzoic Acid, via Modulation of the Root Cell Cycle

The continuous growth of roots depends on their ability to maintain a balanced ratio between cell production and cell differentiation at the tip. This process is regulated by the hormonal balance of cytokinin and auxin. However, other important regulators, such as plant folates, also play a regulatory role. In this study, we investigated the impact of the folate precursor para-aminobenzoic acid (PABA) on root development. Using pharmacological, genetic, and imaging approaches, we show that the growth of Arabidopsis thaliana roots is repressed by either supplementing the growth medium with PABA or overexpressing the PABA synthesis gene GAT-ADCS. This is associated with a smaller root meristem consisting of fewer cells. Conversely, reducing the levels of free root endogenous PABA results in longer roots with extended meristems. We provide evidence that PABA represses Arabidopsis root growth in a folate-independent manner and likely acts through two mechanisms: (i) the G2/M transition of cell division in the root apical meristem and (ii) promoting premature cell differentiation in the transition zone. These data collectively suggest that PABA plays a role in Arabidopsis root growth at the intersection between cell division and cell differentiation.

The unconventional prefoldin RPB5 interactor mediates the gravitropic response by modulating cytoskeleton organization and auxin transport in Arabidopsis

Gravity-induced root curvature involves the asymmetric distribution of the phytohormone auxin. This response depends on the concerted activities of the auxin transporters such as PIN-FORMED (PIN) proteins for auxin efflux and AUXIN RESISTANT 1 (AUX1) for auxin influx. However, how the auxin gradient is established remains elusive. Here we identified a new mutant with a short root, strong auxin distribution in the lateral root cap and an impaired gravitropic response. The causal gene encoded an Arabidopsis homolog of the human unconventional prefoldin RPB5 interactor (URI). AtURI interacted with prefoldin 2 (PFD2) and PFD6, two β-type PFD members that modulate actin and tubulin patterning in roots. The auxin reporter DR5_rev :GFP showed that asymmetric auxin redistribution after gravistimulation is disordered in aturi-1 root tips. Treatment with the endomembrane protein trafficking inhibitor brefeldin A indicated that recycling of the auxin transporter PIN2 is disrupted in aturi-1 roots as well as in pfd mutants. We propose that AtURI cooperates with PFDs to recycle PIN2 and modulate auxin distribution.

Genome-Wide Identification of Auxin Response Factors in Peanut (Arachis hypogaea L.) and Functional Analysis in Root Morphology

Auxin response factors (ARFs) play important roles in plant growth and development; however, research in peanut (Arachis hypogaea L.) is still lacking. Here, 63, 30, and 30 AhARF genes were identified from an allotetraploid peanut cultivar and two diploid ancestors (A. duranensis and A. ipaensis). Phylogenetic tree and gene structure analysis showed that most AhARFs were highly similar to those in the ancestors. By scanning the whole-genome for ARF-recognized cis-elements, we obtained a potential target gene pool of AhARFs, and the further cluster analysis and comparative analysis showed that numerous members were closely related to root development. Furthermore, we comprehensively analyzed the relationship between the root morphology and the expression levels of AhARFs in 11 peanut varieties. The results showed that the expression levels of AhARF14/26/45 were positively correlated with root length, root surface area, and root tip number, suggesting an important regulatory role of these genes in root architecture and potential application values in peanut breeding.

Characterization of a Novel Creeping Tartary Buckwheat (Fagopyrum tataricum) Mutant lazy1

Gravity is known as an important environmental factor involved in the regulation of plant architecture. To identify genes related to the gravitropism of Tartary buckwheat, a creeping line was obtained and designated as lazy1 from the mutant bank by ⁶⁰Co-γ ray radiation. Genetic analysis indicated that the creeping phenotype of lazy1 was attributed to a single recessive locus. As revealed by the horizontal and inverted suspension tests, lazy1 was completely lacking in shoot negative gravitropism. The creeping growth of lazy1 occurred at the early seedling stage, which could not be recovered by exogenous heteroauxin, hormodin, α-rhodofix, or gibberellin. Different from the well-organized and equivalent cell elongation of wild type (WT), lazy1 exhibited dilated, distorted, and abnormally arranged cells in the bending stem. However, no statistical difference of indole-3-acetic acid (IAA) levels was found between the far- and near-ground bending sides in lazy1, which suggests that the asymmetric cell elongation of lazy1 was not induced by auxin gradient. Whereas, lazy1 showed up-expressed gibberellin-regulated genes by quantitative real-time PCR (qRT-PCR) as well as significantly higher levels of gibberellin, suggesting that gibberellin might be partly involved in the regulation of creeping growth in lazy1. RNA sequencing (RNA-seq) identified a number of differentially expressed genes (DEGs) related to gravitropism at stages I (before bending), II (bending), and III (after bending) between WT and lazy1. Venn diagram indicated that only Pectate lyase 5 was down-expressed at stages I [Log₂ fold change (Log₂FC): -3.20], II (Log₂FC: -4.97), and III (Log₂FC: -1.23) in lazy1, compared with WT. Gene sequencing revealed that a fragment deletion occurred in the coding region of Pectate lyase 5, which induced the destruction of a pbH domain in Pectate lyase 5 of lazy1. qRT-PCR indicated that Pectate lyase 5 was extremely down-expressed in lazy1 at stage II (0.02-fold of WT). Meanwhile, lazy1 showed the affected expression of lignin- and cellulose-related genes and cumulatively abnormal levels of pectin, lignin, and cellulose. These results demonstrate the possibility that Pectate lyase 5 functions as the key gene that could mediate primary cell wall metabolism and get involved in the asymmetric cell elongation regulation of lazy1.

The role of AUX1 during lateral root development in the domestication of the model C4 grass Setaria italica

C4 photosynthesis increases the efficiency of carbon fixation by spatially separating high concentrations of molecular oxygen from Rubisco. The specialized leaf anatomy required for this separation evolved independently many times. The morphology of C4 root systems is also distinctive and adapted to support high rates of photosynthesis; however, little is known about the molecular mechanisms that have driven the evolution of C4 root system architecture. Using a mutant screen in the C4 model plant Setaria italica, we identify Siaux1-1 and Siaux1-2 as root system architecture mutants. Unlike in S. viridis, AUX1 promotes lateral root development in S. italica. A cell by cell analysis of the Siaux1-1 root apical meristem revealed changes in the distribution of cell volumes in all cell layers and a dependence of the frequency of protophloem and protoxylem strands on SiAUX1. We explore the molecular basis of the role of SiAUX1 in seedling development using an RNAseq analysis of wild-type and Siaux1-1 plants and present novel targets for SiAUX1-dependent gene regulation. Using a selection sweep and haplotype analysis of SiAUX1, we show that Hap-2412TT in the promoter region of SiAUX1 is an allele which is associated with lateral root number and has been strongly selected for during Setaria domestication.

Plant Gravitropism: From Mechanistic Insights into Plant Function on Earth to Plants Colonizing Other Worlds

Gravitropism, the growth of roots and shoots toward or away from the direction of gravity, has been studied for centuries. Such studies have not only led to a better understanding of the gravitropic process itself, but also paved new paths leading to deeper mechanistic insights into a wide range of research areas. These include hormone biology, cell signal transduction, regulation of gene expression, plant evolution, and plant interactions with a variety of environmental stimuli. In addition to contributions to basic knowledge about how plants function, there is accumulating evidence that gravitropism confers adaptive advantages to crops, particularly under marginal agricultural soils. Therefore, gravitropism is emerging as a breeding target for enhancing agricultural productivity. Moreover, research on gravitropism has spawned several studies on plant growth in microgravity that have enabled researchers to uncouple the effects of gravity from other tropisms. Although rapid progress on understanding gravitropism witnessed during the past decade continues to be driven by traditional molecular, physiological, and cell biological tools, these tools have been enriched by technological innovations in next-generation omics platforms and microgravity analog facilities. In this chapter, we review the field of gravitropism by highlighting recent landmark studies that have provided unique insights into this classic research topic while also discussing potential contributions to agriculture on Earth and beyond.

Permissive action of H2O2 mediated ClUGT75 expression for auxin glycosylation and Al3+- tolerance in watermelon

Although Al³⁺-toxicity is one of the limiting factors for crop production in acidic soils, little is known about the Al³⁺-tolerance mechanism in watermelon, a fairly acid-tolerant crop. This work aimed to identify the interaction between the H₂O₂ scavenging pathway and auxin glycosylation relevant to watermelon Al³⁺-tolerance. By analyzing expressions of hormone-related ClUGTs and antioxidant enzyme genes in Al³⁺-tolerant (ZJ) and Al³⁺-sensitive (NBT) cultivars, we identified ClUGT75s (B1, B2, and D1) and ClSOD1-2-ClCAT as crucial components associated with Al³⁺-tolerance. Al³⁺-stress significantly increased H₂O₂ content by 92.7% in NBT and 42.3% in ZJ, accompanied by less Al³⁺-, auxin (IAA and IBA), and MDA contents in ZJ than NBT. These findings coincided with significant ClSOD1-2 expression and stable dismutation activity in NBT than ZJ. Hence, higher H₂O₂ content in the root apex of NBT than ZJ correlated with a significant increase in auxin content and ClSOD1-2 up-regulation. Moreover, Al³⁺-activated ClUGT75D1 and ClUGT75B2 in ZJ coincided with no considerable change in IBA content, suggesting that glycosylation-mediated changes in IBA content might be relevant to Al³⁺-tolerance in watermelon. Furthermore, exogenous H₂O₂ and IBA indicated ClUGT75D1 modulating IBA is likely dependent on H₂O₂ background. We hypothesize that a higher H₂O₂ level in NBT represses ClUGT75, resulting in increased auxin than those in ZJ roots. Thus, excess in both H₂O₂ and auxin aggravated the inhibition of root elongation under Al³⁺-stress. Our findings provide insights on the permissive action of H₂O₂ in the mediation of auxin glycosylation by ClUGT75 in root apex for Al³⁺-tolerance in watermelon.

Understanding the Intricate Web of Phytohormone Signalling in Modulating Root System Architecture

Root system architecture (RSA) is an important developmental and agronomic trait that is regulated by various physical factors such as nutrients, water, microbes, gravity, and soil compaction as well as hormone-mediated pathways. Phytohormones act as internal mediators between soil and RSA to influence various events of root development, starting from organogenesis to the formation of higher order lateral roots (LRs) through diverse mechanisms. Apart from interaction with the external cues, root development also relies on the complex web of interaction among phytohormones to exhibit synergistic or antagonistic effects to improve crop performance. However, there are considerable gaps in understanding the interaction of these hormonal networks during various aspects of root development. In this review, we elucidate the role of different hormones to modulate a common phenotypic output, such as RSA in Arabidopsis and crop plants, and discuss future perspectives to channel vast information on root development to modulate RSA components.

Auxin and Root Gravitropism: Addressing Basic Cellular Processes by Exploiting a Defined Growth Response

Root architecture and growth are decisive for crop performance and yield, and thus a highly topical research field in plant sciences. The root system of the model plant Arabidopsis thaliana is the ideal system to obtain insights into fundamental key parameters and molecular players involved in underlying regulatory circuits of root growth, particularly in responses to environmental stimuli. Root gravitropism, directional growth along the gravity, in particular represents a highly sensitive readout, suitable to study adjustments in polar auxin transport and to identify molecular determinants involved. This review strives to summarize and give an overview into the function of PIN-FORMED auxin transport proteins, emphasizing on their sorting and polarity control. As there already is an abundance of information, the focus lies in integrating this wealth of information on mechanisms and pathways. This overview of a highly dynamic and complex field highlights recent developments in understanding the role of auxin in higher plants. Specifically, it exemplifies, how analysis of a single, defined growth response contributes to our understanding of basic cellular processes in general.

Folates in legume root nodules

Folates are multifunctional metabolites in plants that are essential for cell division, nucleic acids and amino acid synthesis. During symbiotic nitrogen fixation in legumes, these cofactors are needed for de novo purine biosynthesis, meaning that changes in the folate pools could directly affect the flow of fixed nitrogen to the plant. Its role related to symbiotic nitrogen fixation has not been yet explored, but recent data suggest a relevant role during the first steps. Transcriptomic, metabolomic and proteomic analyses indicate that folates are accumulated in symbiotic plant tissue, as they are involved, not only in de novo purines biosynthesis, but in nitrogen translocation, endoreduplication and phytohormones biosynthesis. Understanding the possible implication of folate pools during the nitrogen fixation and assimilation, might aid for new engineering targets, in relation to the two transformylations or the production of glycine by serine hydroxymethyltransferase during the de novo purine biosynthetic pathway. In this review, we intend to deliver and discuss the available evidence that support a relevant role of folates during the symbiotic nitrogen fixation.

Comparative gene expression analysis reveals that multiple mechanisms regulate the weeping trait in Prunus mume

Prunus mume (also known as Mei) is an important ornamental plant that is popular with Asians. The weeping trait in P. mume has attracted the attention of researchers for its high ornamental value. However, the formation of the weeping trait of woody plants is a complex process and the molecular basis of weeping stem development is unclear. Here, the morphological and histochemical characteristics and transcriptome profiles of upright and weeping stems from P. mume were studied. Significant alterations in the histochemical characteristics of upright and weeping stems were observed, and the absence of phloem fibres and less xylem in weeping stems might be responsible for their inability to resist gravity and to grow downward. Transcriptome analysis showed that differentially expressed genes (DEGs) were enriched in phenylpropanoid biosynthesis and phytohormone signal transduction pathways. To investigate the differential responses to hormones, upright and weeping stems were treated with IAA (auxin) and GA₃ (gibberellin A3), respectively, and the results revealed that weeping stems had a weaker IAA response ability and reduced upward bending angles than upright stems. On the contrary, weeping stems had increased upward bending angles than upright stems with GA₃ treatment. Compared to upright stems, interestingly, DEGs associated with diterpenoid biosynthesis and phenylpropanoid biosynthesis were significantly enriched after being treated with IAA, and expression levels of genes associated with phenylpropanoid biosynthesis, ABC transporters, glycosylphosphatidylinositol (GPI)—anchor biosynthesis were altered after being treated with GA₃ in weeping stems. Those results reveal that multiple molecular mechanisms regulate the formation of weeping trait in P. mume, which lays a theoretical foundation for the cultivation of new varieties.

NMR spectroscopy analysis reveals differential metabolic responses in arabidopsis roots and leaves treated with a cytokinesis inhibitor

In plant cytokinesis, de novo formation of a cell plate evolving into the new cell wall partitions the cytoplasm of the dividing cell. In our earlier chemical genomics studies, we identified and characterized the small molecule endosidin-7, that specifically inhibits callose deposition at the cell plate, arresting late-stage cytokinesis in arabidopsis. Endosidin-7 has emerged as a very valuable tool for dissecting this essential plant process. To gain insights regarding its mode of action and the effects of cytokinesis inhibition on the overall plant response, we investigated the effect of endosidin-7 through a nuclear magnetic resonance spectroscopy (NMR) metabolomics approach. In this case study, metabolomics profiles of arabidopsis leaf and root tissues were analyzed at different growth stages and endosidin-7 exposure levels. The results show leaf and root-specific metabolic profile changes and the effects of endosidin-7 treatment on these metabolomes. Statistical analyses indicated that the effect of endosidin-7 treatment was more significant than the developmental impact. The endosidin-7 induced metabolic profiles suggest compensations for cytokinesis inhibition in central metabolism pathways. This study further shows that long-term treatment of endosidin-7 profoundly changes, likely via alteration of hormonal regulation, the primary metabolism of arabidopsis seedlings. Hormonal pathway-changes are likely reflecting the plant’s responses, compensating for the arrested cell division, which in turn are leading to global metabolite modulation. The presented NMR spectral data are made available through the Metabolomics Workbench, providing a reference resource for the scientific community.

A Role for Auxin in Ethylene-Dependent Inducible Aerenchyma Formation in Rice Roots

Internal oxygen diffusion from shoot to root tips is enhanced by the formation of aerenchyma (gas space) in waterlogged soils. Lysigenous aerenchyma is created by programmed cell death and subsequent lysis of the root cortical cells. Rice (Oryza sativa) forms aerenchyma constitutively under aerobic conditions and increases its formation under oxygen-deficient conditions. Recently, we have demonstrated that constitutive aerenchyma formation is regulated by auxin signaling mediated by Auxin/indole-3-acetic acid protein (AUX/IAA; IAA). While ethylene is involved in inducible aerenchyma formation, the relationship of auxin and ethylene during aerenchyma formation remains unclear. Here, we examined the effects of oxygen deficiency and ethylene on aerenchyma formation in the roots of a rice mutant (iaa13) in which auxin signaling is suppressed by a mutation in the degradation domain of IAA13 protein. The results showed that AUX/IAA-mediated auxin signaling contributes to ethylene-dependent inducible aerenchyma formation in rice roots. An auxin transport inhibitor abolished aerenchyma formation under oxygen-deficient conditions and reduced the expression of genes encoding ethylene biosynthesis enzymes, further supporting the idea that auxin is involved in ethylene-dependent inducible aerenchyma formation. Based on these studies, we propose a mechanism that underlies the relationship between auxin and ethylene during inducible aerenchyma formation in rice roots.

Settling for Less: Do Statoliths Modulate Gravity Perception?

Plants orientate their growth either towards (in roots) or away from (in shoots) the Earth's gravitational field. While we are now starting to understand the molecular architecture of these gravity response pathways, the gravity receptor remains elusive. This perspective looks at the biology of statoliths and suggests it is conceivable that their immediate environment may be tuned to modulate the strength of the gravity response. It then suggests how mutant screens could use this hypothesis to identify the gravity receptor.

A role for the auxin precursor anthranilic acid in root gravitropism via regulation of PIN-FORMED protein polarity and relocalisation in Arabidopsis

distribution of auxin within plant tissues is of great importance for developmental plasticity, including root gravitropic growth. Auxin flow is directed by the subcellular polar distribution and dynamic relocalisation of auxin transporters such as the PIN-FORMED (PIN) efflux carriers, which can be influenced by the main natural plant auxin indole-3-acetic acid (IAA). Anthranilic acid (AA) is an important early precursor of IAA and previously published studies with AA analogues have suggested that AA may also regulate PIN localisation. Using Arabidopsis thaliana as a model species, we studied an AA-deficient mutant displaying agravitropic root growth, treated seedlings with AA and AA analogues and transformed lines to over-produce AA while inhibiting its conversion to downstream IAA precursors. We showed that AA rescues root gravitropic growth in the AA-deficient mutant at concentrations that do not rescue IAA levels. Overproduction of AA affects root gravitropism without affecting IAA levels. Treatments with, or deficiency in, AA result in defects in PIN polarity and gravistimulus-induced PIN relocalisation in root cells. Our results revealed a previously unknown role for AA in the regulation of PIN subcellular localisation and dynamics involved in root gravitropism, which is independent of its better known role in IAA biosynthesis.

Evolution of folate biosynthesis and metabolism across algae and land plant lineages

Tetrahydrofolate and its derivatives, commonly known as folates, are essential for almost all living organisms. Besides acting as one-carbon donors and acceptors in reactions producing various important biomolecules such as nucleic and amino acids, as well as pantothenate, they also supply one-carbon units for methylation reactions. Plants along with bacteria, yeast and fungi synthesize folates de novo and therefore constitute a very important dietary source of folates for animals. All the major steps of folate biosynthesis and metabolism have been identified but only few have been genetically characterized in a handful of model plant species. The possible differences in the folate pathway between various plant and algal species have never been explored. In this study we present a comprehensive comparative study of folate biosynthesis and metabolism of all major land plant lineages as well as green and red algae. The study identifies new features of plant folate metabolism that might open new directions to folate research in plants.

AtDAT1 Is a Key Enzyme of D-Amino Acid Stimulated Ethylene Production in Arabidopsis thaliana

D-Enantiomers of proteinogenic amino acids (D-AAs) are found ubiquitously, but the knowledge about their metabolism and functions in plants is scarce. A long forgotten phenomenon in this regard is the D-AA-stimulated ethylene production in plants. As a starting point to investigate this effect, the Arabidopsis accession Landsberg erecta (Ler) got into focus as it was found defective in metabolizing D-AAs. Combining genetics and molecular biology of T-DNA insertion lines and natural variants together with biochemical and physiological approaches, we could identify AtDAT1 as a major D-AA transaminase in Arabidopsis. Atdat1 loss-of-function mutants and Arabidopsis accessions with defective AtDAT1 alleles were unable to produce the metabolites of D-Met, D-Ala, D-Glu, and L-Met. This result corroborates the biochemical characterization, which showed highest activity of AtDAT1 using D-Met as a substrate. Germination of seedlings in light and dark led to enhanced growth inhibition of atdat1 mutants on D-Met. Ethylene measurements revealed an increased D-AA stimulated ethylene production in these mutants. According to initial working models of this phenomenon, D-Met is preferentially malonylated instead of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC). This decrease of ACC degradation should then lead to the increase of ethylene production. We could observe a reciprocal relation of malonylated methionine and ACC upon D-Met application and significantly more malonyl-methionine in atdat1 mutants. Unexpectedly, the malonyl-ACC levels did not differ between mutants and wild type. With AtDAT1, the first central enzyme of plant D-AA metabolism was characterized biochemically and physiologically. The specific effects of D-Met on ACC metabolism, ethylene production, and plant development of dat1 mutants unraveled the impact of AtDAT1 on these processes; however, they are not in full accordance to previous working models. Instead, our results imply the influence of additional factors or processes on D-AA-stimulated ethylene production, which await to be uncovered.